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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.
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Friday, June 30 • 15:20 - 16:35
P22: Enhancing the Multi-omics Visualization Platform (MVP) Plug-in for Galaxy-based Applications

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Thomas McGowan 1,*, James Johnson 1, Pratik Jagtap 2,* 

 1 : University of Minnesota Supercomputing Institute  (MSI) 
 2 : Department of Biochemistry, Molecular Biology and Biophysics (BMBB), University of Minnesota
 * : Corresponding author

The Multi-omics Visualization Platform (MVP) visualization plug-in for Galaxy allows users to visually explore the peptides identified by mass spectrometry. The mass spectrometry data is queried from a Galaxy SQLite dataprovider from mz.sqlite datasets generated from mzid (mzIdentML) datasets. MVP provides a variety of filters to allow the user to select peptides of interest. A selected peptide can be viewed in a variety of contexts. The peptide identification can be verified visually by viewing individual Peptide Spectral Matches (PSMs) in the Lorikeet scan viewer. The protein view shows the selected peptide aligned to an identification search protein along with the coverage of other identified peptides. If a search protein is a variant determined from RNAseq analysis of the sample, the protein view may show the variation from a reference protein. If genomic mapping is available for the protein, MVP displays bars along the protein for each exon sequence; clicking on the bar will zoom an IGV browser to that genomic location. IGV can then provide genomic context with concurrent display of RNAseq alignments, RNAseq variants, along with a proBAM or proBED alignment of the peptides identified from mass spectrometry. 

avatar for James Johnson

James Johnson

Minnesota Supercomputing Institute, University of Minnesota

Friday June 30, 2017 15:20 - 16:35
Le Corum Le Corum

Attendees (4)